Chlorine adsorption on Au(111): chlorine overlayer or surface chloride?

We report the first scanning tunneling microscope (STM) investigation, combined with density functional theory calculations, to resolve controversy regarding the bonding and structure of chlorine adsorbed on Au(111). STM experiments are carried out at 120 K to overcome instability caused by mobile species upon chlorine adsorption at room temperature. Chlorine adsorption initially lifts the herringbone reconstruction. At low coverages (<0.33 ML), chlorine binds to the top of Au(111)-(1 x 1) surface and leads to formation of an overlayer with (square root(3) x square root(3))R30 degree structure at 0.33 ML. At higher coverages, packing chlorine into an overlayer structure is no longer favored. Gold atoms incorporate into a complex superlattice of a Au-Cl surface compound.     

How large is the static electric (hyper)polarizability anisotropy in HXeI?

An extensive conventional ab initio and density functional theory investigation reveals that HXeI is a polar molecule with large multipole moments and highly anisotropic (hyper)polarizability. At the CCSD(T) level of theory our best values for the mean (hyper)polarizability are alphae(2)a(0) (2)E(h) (-1)=101.46, betae(3)a(0) (3)E(h) (-2)=-850.7, and gammae(4)a(0) (4)E(h) (-3)=18.7x10(3). The corresponding anisotropies are Deltaalphae(2)a(0) (2)E(h) (-1)=119.66, Deltabetae(3)a(0) (3)E(h) (-2)=-2518.7, Delta(1)gammae(4)a(0) (4)E(h) (-3)=-249.1x10(3), and Delta(2)gammae(4)a(0) (4)E(h) (-3)=-99.6x10(3). The longitudinal components of the (hyper)polarizability are dominant. Our value for the anisotropy of the dipole polarizability is considerably larger than the recent empirical estimate of 22.9 e(2)a(0) (2)E(h) (-1) [N. H. Nahler et al., J. Chem. Phys. 119, 224 (2003)]. The results of the insertion of Xe into HI are quantified by the calculation of the differential (hyper)polarizability at the MP2 level of theory: alpha(diff) identical withalpha(HXeI)-alpha(HI)-alpha(Xe)=36.29 e(2)a(0) (2)E(h) (-1) and gamma(diff) identical with gamma(HXeI)-gamma(HI)-gamma(Xe)=18.1x10(3) e(4)a(0) (4)E(h) (-3).     

Self-sorting: the exception or the rule?

In this paper, we pose the question of whether self-sorting in designed systems is exceptional behavior or whether it is likely to become a more general phenomenon governing molecular recognition and self-assembly. To address this question we prepared a mixture comprising two of Davis' self-assembled ionophores, Rebek's tennis ball and calixarene tetraurea capsule, Meijer's ureidopyrimidinone, Reinhoudt's calixarene bis(rosette), and two molecular clips in CDCl(3) solution and observed the behavior of this ensemble by (1)H NMR. As hypothesized, high-fidelity self-sorting behavior was observed. The influence of several key variables-temperature, concentration, equilibrium constants, and the presence of competitors-on the fidelity of self-sorting is described. These results show that self-sorting is neither the exception nor the rule. They suggest, however, that the subset of known molecular aggregates that exceed the criteria required for thermodynamic self-sorting is larger than previously appreciated and potentially quite broad.     

Hydronium ion complex of 18-crown-6: where are the protons? A density functional study of static and dynamic properties

A quantum-chemical study employing the BLYP density functional is reported for the complex of H3O+ with 18-crown-6. According to a Car-Parrinello molecular dynamics (CPMD) study at 340 K, the complex is quite flexible, and is characterized by three quasi-linear (two-center) hydrogen-bond interactions for most of the time. On a time scale of 10 ps, frequent inversions of H3O+ are observed, as well as two 120 degrees rotations switching the hydrogen bonds from one set of crown-ether O atoms to the other. These results are consistent with density-functional studies of stationary points on the potential energy surface, which show how the crown "catalyzes" the guest's inversion. Two close-lying minima are characterized, as well as two distinct transition states connecting them, either via H3O+ inversion or rotation, with barriers of 1.0 and 4.6 kcal/mol, respectively, at the BLYP/II'//BLYP/6-31G level. Orbital interactions between lone pairs on ether O atoms and hydronium sigma(OH) antibonding orbitals are important factors for the directionality of the hydrogen bonds.     

IrII(ethene): metal or carbon radical?

One-electron oxidation of [(Me(n)tpa)Ir(I)(ethene)]+ complexes (Me(3)tpa = N,N,N-tri(6-methyl-2-pyridylmethyl)amine; Me(2)tpa = N-(2-pyridylmethyl)-N,N,-di[(6-methyl-2-pyridyl)methyl]-amine) results in relatively stable, five-coordinate Ir(II)-olefin species [(Me(n)tpa)Ir(II)(ethene)](2+) (1(2+): n = 3; 2(2+): n = 2). These contain a "vacant site" at iridium and a "non-innocent" ethene fragment, allowing radical type addition reactions at both the metal and the ethene ligand. The balance between metal- and ligand-centered radical behavior is influenced by the donor capacity of the solvent. In weakly coordinating solvents, 1(2+) and 2(2+) behave as moderately reactive metallo-radicals. Radical coupling of 1(2+) with NO in acetone occurs at the metal, resulting in dissociation of ethene and formation of the stable nitrosyl complex [(Me(3)tpa)Ir(NO)](2+) (6(2+)). In the coordinating solvent MeCN, 1(2+) generates more reactive radicals; [(Me(3)tpa)Ir(MeCN)(ethene)](2+) (9(2+)) by MeCN coordination, and [(Me(3)tpa)Ir(II)(MeCN)](2+) (10(2+)) by substitution of MeCN for ethene. Complex 10(2+) is a metallo-radical, like 1(2+) but more reactive. DFT calculations indicate that 9(2+) is intermediate between the slipped-olefin Ir(II)(CH(2)=CH(2)) and ethyl radical Ir(III)-CH(2)-CH(2). resonance structures, of which the latter prevails. The ethyl radical character of 9(2+) allows radical type addition reactions at the ethene ligand. Complex 2(2+) behaves similarly in MeCN. In the absence of further reagents, 1(2+) and 2(2+) convert to the ethylene bridged species [(Me(n)tpa)(MeCN)Ir(III)(mu(2)-C(2)H(4))Ir(III)(MeCN)(Me(3)tpa)](4+) (n = 3: 3(4+); n = 2: 4(4+)) in MeCN. In the presence of TEMPO (2,2,6,6-tetramethyl-1-piperidinyloxo), formation of 3(4+) from 1(2+) in MeCN is completely suppressed and only [(Me(3)tpa)Ir(III)(TEMPO(-))(MeCN)](2+) (7(2+)) is formed. This is thought to proceed via radical coupling of TEMPO at the metal center of 10(2+). In the presence of water, hydrolysis of the coordinated acetonitrile fragment of 7(2+) results in the acetamido complex [(Me(3)tpa)Ir(III)(NHC(O)CH(3)))(TEMPOH)](2+) (8(2+)).     

Single‐cell gel electrophoresis (the comet assay): Loops or fragments?

Single-cell gel electrophoresis, or the comet assay, is widely used to measure DNA damage and repair. Upon electrophoresis, the DNA of lysed, agarose-embedded cells known as nucleoids, extends towards the anode in a structure resembling a comet, the relative intensity of the tail reflecting the frequency of DNA breaks. The structural organization of the DNA within comet preparations is not fully understood. We have used fluorescent in situ hybridization with large-insert genomic probes and human Cot-I DNA to investigate whether the production of the comet tail is simply explained by the relaxation of supercoiled DNA loops. We find that, under neutral electrophoresis conditions, when the tail and head DNA are double-stranded, the probed sequence of DNA is seen as a linear array, consistent with extension from a fixed point on the nuclear core or matrix. After alkaline electrophoresis, the appearance of the fluorescent probes suggests that linear DNA has coalesced into a granular form.     

The inhibition of hydrogen peroxide reduction at low potentials on Pt(111): Hydrogen adsorption or interfacial charge?

The hydrogen peroxide reduction reaction (HPRR) on Pt(111) has been studied for the first time in acid to neutral pH values in the absence of anion specific adsorption using the HMRDE configuration. The onset for the reduction is ca. 0.95 V (RHE) for the Pt(111), irrespective of the pH value. At more negative potential values, the reduction is inhibited. It has been found that the diminution of the activity on Pt(111) occurs at the same potential value in the SHE scale for the different pH values. This indicates that this deactivation is not dependent on the hydrogen adsorption process, as has been previously suggested. However, it appears to be related to the interface water reorganization and the potential of zero free charge of the metal surface. In addition, studies in alkaline conditions suggest that the presence of adsorbed OH species promotes the total conversion of hydrogen peroxide to water.     

A theoretical investigation of the interaction between substituted carbonyl derivatives and water: Open or cyclic complexes?

The structures and binding energies of complexes between substituted carbonyl bases and water are the B3LYP/6‐311++G(d,p) computational level. The calculations also include the proton affinity (PA) of the O of the C?O group, the deprotonation enthalpies (DPE) of the CH bonds along a natural bond orbital analysis. The calculations reveal that stable open C?O···H_wO_w as well as cyclic CH···O_wH_w···O?C complexes are formed. The binding energies for the open complexes are linearly related to the PAs, whereas the binding energies for the cyclic complexes depend on both the PA and DPE. Different indicators of hydrogen bonds strength such as electron charge density, intramolecular and intermolecular hyperconjugation energy, occupation of orbitals, and charge transfer show significant differences between open and cyclic complexes. The contraction of the CH bond of the formyl group and the corresponding blue shift of the ν(CH) vibration are explained by the classical trans lone pair effect. In contrast, the elongation or contraction of the CH₃ group involved in the interaction with water results from the variation of the orbital interaction energies from the σ(CH) bonding orbital to the σ* and π* antibonding orbitals of the C?O group. The resulting blue or red shifts of the ν(CH₃) vibrations are calculated in the partially deuterated isotopomers. © 2012 Wiley Periodicals, Inc.     

Proteome-on-a-chip: mirage, or on the horizon?

Proteomics has emerged as the next great scientific challenge in the post-genome era. But even the most basic form of proteomics, proteome profiling, i.e., identifying all of the proteins expressed in a given sample, has proven to be a demanding task. The proteome presents unique analytical challenges, including significant molecular diversity, an extremely wide concentration range, and a tendency to adsorb to solid surfaces. Microfluidics has been touted as being a useful tool for developing new methods to solve complex analytical challenges, and, as such, seems a natural fit for application to proteome profiling. In this review, we summarize the recent progress in the field of microfluidics in four key areas related to this application: chemical processing, sample preconcentration and cleanup, chemical separations, and interfaces with mass spectrometry. We identify the bright spots and challenges for the marriage of microfluidics and proteomics, and speculate on the outlook for progress.     

Fluorescence study of the dynamic interaction between E1(145–162) sequence of hepatitis GB virus C and liposomes

The physicochemical characterization of the peptide sequence E1(145–162) corresponding to the structural protein E1 of the hepatitis G virus was done by studying its interaction with model membranes. Small unilamellar vesicles (SUVs) of dimyristoylphosphatidylglycerol or dimyristoylphosphatidylcholine were chosen as mimetic membranes. Peptide incorporation and location in the phospholipid bilayer was investigated by fluorescence anisotropy with SUVs labeled with diphenylhexatriene (DPH) or trimethylammonium–DPH. The addition of the peptide E1(145–162) showed significant changes in the anisotropy values of the probe located at the air/water interface. These results indicate that the peptide E1(145–162) preferably interacts with the lipid surface without penetrating inside the bilayer. A series of fluorescence experiments based on tryptophan peptide fluorescence were modeled by means of multivariate curve resolution-alternating least squares (MCR-ALS) algorithm to further study the peptide interaction with bilayers at different temperatures. The preliminary results obtained with MCR-ALS showed how the peptide concentration decay is directly linked to the appearance of a new specie, which corresponds to the lipid-peptide binding. These results provide useful information for the design of synthetic immunopeptides that can be incorporated into a liposomal system with potential to promote a direct delivery of the membrane-incorporated immunogen to the immunocompetent cells, thus increasing the immuno response from the host. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Low energy electron diffraction and low energy electron microscopy microspot I/V analysis of the (4 x 4)O structure on Ag(111): surface oxide or reconstruction?

A low energy electron diffraction (LEED) I/V analysis was performed of the (4 x 4) oxygen structure on Ag(111). Two data sets were used, one recorded with a conventional LEED system and a second with a low energy electron microscope (LEEM). The data sets agree well with each other, demonstrating that I/V structure analyses can be performed with the same quality with LEEM as with conventional LEED. The structure obtained confirms the recently proposed model that involves a reconstruction of the Ag(111) surface. Previous models based on a thin layer of Ag(2)O that had been accepted for more than 30 years are disproved. The reconstruction model contains two units of six triangularly arranged Ag atoms and a stacking fault in one half of the unit cell. The six O atoms per unit cell occupy sites in the trenches between the Ag(6) triangles. Small lateral displacements of the Ag atoms lift the mirror symmetry of the structure, leading to two nonequivalent groups of O atoms. The atoms of both groups are located approximately 0.5 Angstrom below the top Ag layer, on fourfold positions with respect to the top layer Ag atoms. Ag-O distances between 2.05 and 2.3 Angstrom are found. The oxygen atoms exhibit large static or dynamic displacements of up to 0.3 Angstrom at 300 K.     

Competition between receptors in dynamic combinatorial libraries: amplification of the fittest?

Dynamic combinatorial chemistry is a powerful tool for the discovery of strong binders (synthetic receptors or ligands) because binding causes a shift in the equilibrium of library members toward those that bind well. Ideally, the best binders are selectively amplified. However, theoretical studies predict this is not always the case. This paper describes the first quantitative experimental evidence proving that, under special circumstances, the preferential amplification of suboptimal synthetic receptors can indeed occur. Our results also demonstrate that reducing the amount of guest in the library can rectify such undesirable behavior and ensures selective amplification of the fittest receptor.     

IrII(ethene): metal or carbon radical? Part II: oxygenation via iridium or direct oxygenation at ethene?

Treatment of [(Me3tpa)IrII(ethene)]2+ (Me(3)tpa =N,N,N-tri(6-methyl-2-pyridylmethyl)amine)(1(2+)) with dioxygen in weakly coordinating solvents results in formation of [(Me3tpa)IrIII(ethene)(superoxo)]2+ (4a2+). In the presence of DMPO (DMPO = 5,5-dimethyl-2-pyrrolidine-1-oxide) DMPO is substituted for ethene, and subsequently oxidized to DMPOX by the superoxo fragment to give [(Me3tpa)IrIII(DMPOX)]2+ (7(2+); DMPOX = 5,5-dimethyl-2-pyrrolidone-1-oxide). In acetonitrile, in the absence of DMPO, oxygenation of 1(2+) to [(Me3tpa)IrIII(formylmethyl)(MeCN)]2+ (2(2+)) is observed. In the presence of DMPO the formation of 2(2+) and 7(2+) is competing. Oxygenation of 1(2+) to 2(2+) may proceed via 4a(2+), involving an insertion mechanism at the metal. However, a mechanism based on olefin ligand non-innocence seems a reasonable alternative. This involves formation of acetonitrile adduct [(Me3tpa)Ir(ethene)(MeCN)]2+ (3(2+)), which has a significant metalla-ethyl radical (IrIII-CH2CH2*) character, allowing attack of 3O2 directly at the ethene ligand. Both pathways are discussed on the basis of experimental observations and DFT geometry optimizations.     

氧化锌有序结构在Au(111)和Cu(111)上的生长

利用NO₂或O₂作为氧化剂,研究了氧化锌在Au(111)和Cu(111)上的生长和结构。NO₂表现了更好的氧化性能,有利于有序氧化锌纳米结构或薄膜的生长。在Au(111)和Cu(111)这两个表面上,化学计量比氧化锌都形成非极性的平面化ZnO(0001)的表面结构。在Au(111)上,NO₂气氛下室温沉积锌倾向于形成双层氧化锌纳米结构;而在更高的沉积温度下,在NO₂气氛中沉积锌则可同时观测到单层和双层氧化锌纳米结构。O₂作为氧化剂时可导致形成亚化学计量比的ZnO_x结构。由于铜和锌之间的强相互作用会促进锌的体相扩散,并且铜表面可以被氧化形成表面氧化物,整层氧化锌在Cu(111)上的生长相当困难。我们通过使用NO₂作为氧化剂解决了这个问题,生长出了覆盖Cu(111)表面的满层有序氧化锌薄膜。这些有序氧化锌薄膜表面显示出莫尔条纹,表明存在一个ZnO和Cu(111)之间的莫尔超晶格。实验上观察到的超晶格结构与最近理论计算提出的Cu(111)上的氧化锌薄膜结构相符,具有最小应力。我们的研究表明,氧化锌薄膜的表界面结构可能会随氧化程度或氧化剂的不同而变化,而Cu(111)的表面氧化也可能影响氧化锌的生长。当Cu(111)表面被预氧化成铜表面氧化物时,ZnO_x的生长模式会发生变化,锌原子会受到铜氧化物晶格的限域形成单位点锌。我们的研究表明了氧化锌的生长需要抑制锌向金属基底的扩散,并阻止亚化学计量比ZnO_x的形成。因此,使用原子氧源有利于在Au(111)和Cu(111)表面上生长有序氧化锌薄膜。     

The electrostatic probe: a tool for the investigation of the Aβ(1-16) peptide deformations using the static modes

We investigate the conformational changes of the Amyloid β(1-16) peptide induced by moving Zn(2+) ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn(2+) ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.